Hey!
I tried reading your messages and couldn't quite understand everything you said, I guess I dont have enough knowlage,
But I do have some experiance with such a case,
As I posted a while ago I've renamed my MobileSubstrate.dylib file by mistake ( which I hope is familiar to what you did)
and eventually manged to solve that problem by uploading a copy of the desired file with the correct name using OpeniBoot's CONSOLE (couldn't get adb to work...)
so if you manage to find a copy of the file you've renamed online you can try doing this:
get into openiboot console in your iphone
use the 'loadibec'/'oibc' ( If forgot which of them does that) to be able to send commands
get a copy of MobileSubstrate.dylib to the folder where your loadibec/oibc is
then use:
!MobileSubstrate.dylib
to upload it to the memory and then, remember the number of bytes the conosle tells you!
use:
fs_add /var FILEPATH/FILENAME 0x09000000 #OfBytes
(example:
fs_add /var Library/MobileSubstrate/MobileSubstrate.dylib 0x09000000 14416)
to copy it from the memory to the filesystem.
done!~
Please note: It might screw some stuff in your iphone even thou it SHOULDN'T as I understood from nickp666 the 'area' of 0x09000000 is safe to upload files to but I cannot promise, but it did work for me :T
Good luck!